Certain cDNA library preparation methods involve fragmenting mRNA and then reverse transcribing the resultant fragments of mRNA to make cDNA. In these methods, cleavage typically occurs at random or semi-random positions and, as such, the population of RNA fragments made by such methods typically contains RNA fragments of different lengths, wherein at least some of the fragments are relatively small, i.e., less than 20 nucleotides in length. These short fragments are problematic because their cDNA copies are amplified very efficiently but their sequences (particularly for fragment that are 10-15 in length) are not always uniquely mappable to a transcriptome. This problem can be potentially avoided by performing a physical size selection of the cDNAs or the amplification products. However, because of the imprecise nature of physical size selection methods it is impossible to eliminate cDNA copies of the shorter RNAs without also eliminating cDNA copies of many of longer RNAs,
A better way for selecting RNA molecules by size is therefore needed.